I know Omni makes OmniPresence, but I want to keep related project files together — I don’t want to have to keep my OmniGraffle files in some separate directory.

It’s in the works! As @funkydan2 mentioned, iCloud Drive and other cloud support is on our roadmap for this year. For what it’s worth, only the iOS app will need to be updated to add this import/export option — the iCloud Drive in OS X Finder’s already compatible with OmniGraffle for Mac files, so you can start sharing OmniGraffle documents across your Macs today.

Is OmniOutliner for OS X also compatible with iCloud Drive? I performed a limited test in which I edited the same OmniOutliner document from two different Macs. I saved the changes on the first one, then I saved the changes on the second one expecting some sort of conflict dialog to appear (try the same thing with TextEdit for an example of what I mean). Not only did I not receive a conflict warning, the changes from the second Mac overwrote the changes from the first one!

Is OmniOutliner for OS X also compatible with iCloud Drive? I performed a limited test in which I edited the same OmniOutliner document from two different Macs. I saved the changes on the first one, then I saved the changes on the second one expecting some sort of conflict dialog to appear (try the same thing with TextEdit for an example of what I mean). Not only did I not receive a conflict warning, the changes from the second Mac overwrote the changes from the first one!

You’re right, iCloud Drive already works great with OmniOutliner for Mac. Files you store in iCloud Drive would only be accessible from other Macs running Yosemite, at least until we roll out built-in iCloud Drive support in OmniOutliner 2 for iOS.

For what it’s worth, there’s not much Omni can do about the specific scenario you’re describing. iCloud Drive (as opposed to CloudKit, the API that underpins it) is pretty primitive by document-syncing standards at the moment. It has no conflict-resolution interface, and will just use the most recent timestamped file as the canonical version of a file when looking at two versions. There’s also no ability to look at previous versions of a file, so far.

This may not be the case forever: CloudKit has APIs for building three-way-merge conflict resolution, better auto-conflict resolution via change tokens, and a few other nice features. There’s no reason Apple couldn’t extend their iCloud Drive service to use these features for doing conflict UIs and the like, but for the moment they’re depending on specific app developers providing their own solutions by using CloudKit directly.

If conflict resolution and version history is important to you right now, I’d suggest sticking with Dropbox for syncing between two Macs since Dropbox has conflict resolution and versions (although that’s not going to help you on iOS).